[2024-01-24 11:51:11,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference
[2024-01-24 11:51:12,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,520] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfb607ce-89ee-4157-99e2-309faaf50518/GCF_002855455.1_ASM285545v1_genomic.fna.gz | prodigal -d GCF_002855455.1_ASM285545v1_genomic.fna/cds.fna -a GCF_002855455.1_ASM285545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:30,229] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:30,229] [INFO] Task started: HMMsearch
[2024-01-24 11:51:30,229] [INFO] Running command: hmmsearch --tblout GCF_002855455.1_ASM285545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/reference_markers.hmm GCF_002855455.1_ASM285545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:30,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:30,492] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbfb607ce-89ee-4157-99e2-309faaf50518/GCF_002855455.1_ASM285545v1_genomic.fna.gz]
[2024-01-24 11:51:30,526] [INFO] Query marker FASTA was written to GCF_002855455.1_ASM285545v1_genomic.fna/markers.fasta
[2024-01-24 11:51:30,526] [INFO] Task started: Blastn
[2024-01-24 11:51:30,526] [INFO] Running command: blastn -query GCF_002855455.1_ASM285545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/reference_markers.fasta -out GCF_002855455.1_ASM285545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:31,049] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:31,053] [INFO] Selected 6 target genomes.
[2024-01-24 11:51:31,053] [INFO] Target genome list was writen to GCF_002855455.1_ASM285545v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:31,058] [INFO] Task started: fastANI
[2024-01-24 11:51:31,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb607ce-89ee-4157-99e2-309faaf50518/GCF_002855455.1_ASM285545v1_genomic.fna.gz --refList GCF_002855455.1_ASM285545v1_genomic.fna/target_genomes.txt --output GCF_002855455.1_ASM285545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:42,175] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:42,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:42,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:42,183] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:51:42,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:42,183] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Natronobacterium gregoryi	strain=SP2	GCA_002855455.1	44930	44930	type	True	100.0	1156	1161	95	conclusive
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	99.9959	1153	1161	95	conclusive
Natronobacterium gregoryi	strain=SP2	GCA_000230715.3	44930	44930	type	True	99.9947	1158	1161	95	conclusive
Natronobacterium gregoryi	strain=SP2	GCA_000337655.1	44930	44930	type	True	99.9314	1120	1161	95	conclusive
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	85.2375	889	1161	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	81.76	762	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:42,185] [INFO] DFAST Taxonomy check result was written to GCF_002855455.1_ASM285545v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:42,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:42,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:42,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/checkm_data
[2024-01-24 11:51:42,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:42,225] [INFO] Task started: CheckM
[2024-01-24 11:51:42,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002855455.1_ASM285545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002855455.1_ASM285545v1_genomic.fna/checkm_input GCF_002855455.1_ASM285545v1_genomic.fna/checkm_result
[2024-01-24 11:52:29,970] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:29,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,995] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:29,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:29,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002855455.1_ASM285545v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:29,996] [INFO] Task started: Blastn
[2024-01-24 11:52:29,996] [INFO] Running command: blastn -query GCF_002855455.1_ASM285545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7df1f169-090c-4dbe-9b6a-87a90de138f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002855455.1_ASM285545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:30,498] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:30,501] [INFO] Selected 8 target genomes.
[2024-01-24 11:52:30,502] [INFO] Target genome list was writen to GCF_002855455.1_ASM285545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:30,507] [INFO] Task started: fastANI
[2024-01-24 11:52:30,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb607ce-89ee-4157-99e2-309faaf50518/GCF_002855455.1_ASM285545v1_genomic.fna.gz --refList GCF_002855455.1_ASM285545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002855455.1_ASM285545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:39,351] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:39,359] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:39,359] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000230715.2	s__Natronobacterium gregoryi	99.9947	1158	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	99.99	99.97	1.00	1.00	4	conclusive
GCF_900104065.1	s__Natronobacterium texcoconense	85.2375	889	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337895.1	s__Halobiforma nitratireducens	82.5195	674	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112205.1	s__Halobiforma haloterrestris	81.8022	759	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	81.7687	751	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000217715.1	s__Halopiger xanaduensis	80.3744	624	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	80.3136	634	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	80.2502	628	1161	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:39,361] [INFO] GTDB search result was written to GCF_002855455.1_ASM285545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:39,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:39,364] [INFO] DFAST_QC result json was written to GCF_002855455.1_ASM285545v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:39,364] [INFO] DFAST_QC completed!
[2024-01-24 11:52:39,364] [INFO] Total running time: 0h1m28s